Abstract

Airborne microorganisms have been studied for centuries, but the majority of this research has relied on cultivation-dependent surveys that may not capture all of the microbial diversity in the atmosphere. As a result, our understanding of airborne microbial ecology is limited despite the relevance of airborne microbes to human health, various ecosystem functions, and environmental quality. Cultivation-independent surveys of small-subunit rRNA genes were conducted in order to identify the types of airborne bacteria and fungi found at a single site (Boulder, CO) and the temporal variability in the microbial assemblages over an 8-day period. We found that the air samples were dominated by ascomycete fungi of the Hypocreales order and a diverse array of bacteria, including members of the proteobacterial and Cytophaga-Flavobacterium-Bacteroides groups that are commonly found in comparable culture-independent surveys of airborne bacteria. Bacterium/fungus ratios varied by 2 orders of magnitude over the sampling period, and we observed large shifts in the phylogenetic diversity of bacteria present in the air samples collected on different dates, shifts that were not likely to be related to local meteorological conditions. We observed more phylogenetic similarity between bacteria collected from geographically distant sites than between bacteria collected from the same site on different days. These results suggest that outdoor air may harbor similar types of bacteria regardless of location and that the short-term temporal variability in airborne bacterial assemblages can be very large.

Taxonomic identities of the clones sequenced from each library. The numbers in parentheses indicate the total number of sequenced clones (out of 768 per library) that were nonchimeric and could be assigned to one of the four taxonomic groups (E < 1e−100).

Major groups of bacteria identified from each clone library. Firmicutes refers to the Bacillus-Clostridium group and CFB refers to the Cytophaga-Flavobacterium-Bacteroides group. The numbers in parentheses indicate the total number of bacterial clones in each library.

Phylogenetic relationships between representative sequences of the dominant airborne bacteria. Boldface type indicates sequences from the present study. Nearest-neighbor bacterial isolates are indicated by italics. Asterisks indicate representative sequences from other studies of airborne bacteria; the GenBank accession numbers starting with AY and DQ indicate sequences obtained from outside air samples by Angenent et al. () and Brodie et al. (), respectively. Sequences were aligned by using MUSCLE (), and the neighbor-joining tree was constructed by using PAUP (). The archaeon, Haloferax volcanii, was included as the outgroup (not shown).

Weighted UniFrac distance between the bacterial (A) and fungal (B) sequences identified from outside air samples collected in Boulder, CO (the present study, identified by dates in May); New Orleans, LA (Rodríguez-Hernández, unpublished data); and an undisclosed location in the midwestern United States (). Since very few fungal sequences were identified in the libraries constructed from the New Orleans air, these samples were not included in the fungal UniFrac analyses. For the Boulder sequences, we averaged the calculated distances from the forward and reverse reads from each sample since the two directions yielded very similar results.